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marrink-lab / bentopy

Packs stuff in boxes
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Integration example test and tutorial #3

Open ma3ke opened 8 months ago

ma3ke commented 8 months ago

We want to create a tutorial workflow that introduces all parts of the project and how they can be applied together. Though the tutorial is written toward those who want to learn how to use Bentopy for their workflows, the sequence of steps serves as an integration test as well. This both tests many/most of the features this project implements, and requires the tutorial to be continuously up-to-date and in a working state.

Structure

I propose the structure is roughly as follows:

  1. Introduction
  2. Installation
  3. Preparation of the input files, structures
  4. Packing
  5. Rendering the placements
    • Including some notes on how one may render a part of a packing for inspection.
  6. Energy minimization, noticing problems (collisions? see #2)
  7. Solvation
  8. Equilibration and a short production run.

These steps can be expressed as an executable notebook, and this notebook can be rendered in a wiki-like format to make it accessible in a nice manner to readers.

ma3ke commented 8 months ago

Since bentopy can be used for setting up both CG and AA[^1] systems, that raises the question which of these to discuss in a tutorial. Packing a CG system has some advantages in viewing the large structures: the smaller number of patricles are easier to visualize. But doing so could foster the perception that CG is the only use case, which is simply not the case.

Perhaps we can just do... both. This demonstrates bentopy as a simulation-scale/force-field agnostic tool, while catering to the context & prior knowledge of whoever is interested.

Most likely I will write it all into a single document, with a # id-link to the relevent sections, much like a choose your own adventure book ;)

[^1]: Or whatever, really as long as there is a structure file for it.